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Easy enough to say in the mountains, harder to say in the meadows, pretty dangerous to do in the flatlands.

If you're a 'full time' hiker building up immunity over a decade or so in primarily remote places... I can buy the argument.
But for most of us folks trotting out to the woods for a week or less once or twice a year probably not any chance of building up enough immunity for most places.

What's a sitting? In summer it is not difficult to consume 7 liters of water a day for me when hiking long hours.
Maybe no biggie (on paper) to hit that source once, but day after day for weeks?

" The data on Giardia and Cryptosporidium are similar: A study in the popular magazine Backpackeragain only found pathogens in a minority of sampled sites, with the highest recorded concentration still so dilute that obtaining an infective dose would require consuming 7 liters of water in one sitting."

Either way;
This seems like the most accurate takeaway from the article overall:

"If the real danger comes from eating after a trip to the cathole, then that’s the point thatshould be emphasized—not an unsubstantiated view of all water in the mountains as suspect. In all likelihood, it’s not the water that’s gross. It’s you. "

I think the article should come with a litany of qualifiers. What if you're on immunosuppressants? What if your health is compromised in some other form or fashion?

I don't "need" to wear a seatbelt when I drive, I only "need" one in case of an accident. The rest of the time I wear one for insurance.

Same thing goes for filtering water. With most filters rated for thousands upon thousands of gallons one unit is, essentially, a "lifetime use" item if properly cared for. If it keeps me from getting sick just once, it's well worth it. If it keeps that one illness from ruining a trip, then it's worth even more.

1) The odds of getting a waterbourne illness from any one source is overwhelmingly low.
2) The majority of illness that are blamed on "bad water" are actually transmitted by contact with infected people or contaminated surfaces. Proper hand washing with honest to goodness soap is far more effective at reducing the spread of pathogens than water treatment.
3) Most commercial filters do not protect against viruses like Noro virus that is ever present on major trails.
4) It you are unable to treat your water, just drink it. Dehydration is generally more dangerous to the average hiker than waterbourne contaminants.
5) All that said I still treat my water, because I think it's easy and a smart thing to do.

I make a judgement call. I mostly worry only about water quality staring in Virginia and ending at Vermont. In the middle states I'll opt to filter more often then not. Although even in the mid Atlantic, there are a fair number of good spring sources. We are truly blessed with good water along the majority of the AT.

I probably treated less than 10% of the water I drank from GA to ME. If it was coming from a spring or a pipe in the side of a mtn, I drank it without thinking. If I was at lower elevations and especially around livestock pastures, I would filter. The few times I drank from ponds, especially in ME, I filtered. I knew I was rolling the dice a bit, but never had any issues.

On my 2013 thru hike, I didn't filter or treat my water until I reached Pennsylvania. I believe you need to look at each water source and make an independent decision. If its coming out of the rock from a spring, then there is no reason to treat or filter. If it is a stream, river, or other water source where animals or humans can defecate, then you probably should treat or filter to be safe (although, more likely than not you will be ok).

In high school and college I never filtered. With so many people on the trails now and the amount of TP laying around. I filter. I have had had amoeba 3 times (overseas) giardia several times. I am not playing roulette anymore. If people want to drink straight from the river I wont stop them but I am carrying a filter.

As a biology teacher, I'd say that you're taking your chances with not filtering. You may be fine for quite a while from only backcountry sources...until you're not and you have a nasty case of giardensis or amoebic dysentery from a source that "looked fine". You'll notice that the article goes on about the "lack of evidence" of contamination in backcountry water sources, then tries to use a sub-set of that same evidence to claim it's not a problem. Worse, they use some fairly misleading evidence. The Sierra Nevada study they site, you'll note, only did relatively thorough testing of the hikers themselves for illness, while testing only three water sources once a week for 10 weeks. That's hardly conclusive, and they still documented a 5.7% infection rate with actual G. lamblia. Given what I know about microbes and the probabilities of picking up something really nasty (and possibly dangerous) I'll be filtering every drop I drink.

Strategy without tactics is the slowest route to victory. Tactics without strategy is the noise before defeat.
Sun Tzu, The Art of War.